diff --git a/include/caffe/data_layers.hpp b/include/caffe/data_layers.hpp
index 1f154408c27..2bb9d948169 100644
--- a/include/caffe/data_layers.hpp
+++ b/include/caffe/data_layers.hpp
@@ -171,6 +171,8 @@ class HDF5DataLayer : public Layer<Dtype> {
   unsigned int current_file_;
   hsize_t current_row_;
   std::vector<shared_ptr<Blob<Dtype> > > hdf_blobs_;
+  std::vector<unsigned int> data_permutation_;
+  std::vector<unsigned int> file_permutation_;
 };
 
 /**
diff --git a/src/caffe/layers/hdf5_data_layer.cpp b/src/caffe/layers/hdf5_data_layer.cpp
index 1ceb6c24431..1d3dc1e62ac 100644
--- a/src/caffe/layers/hdf5_data_layer.cpp
+++ b/src/caffe/layers/hdf5_data_layer.cpp
@@ -14,9 +14,9 @@
 #include "hdf5_hl.h"
 #include "stdint.h"
 
+#include "caffe/data_layers.hpp"
 #include "caffe/layer.hpp"
 #include "caffe/util/io.hpp"
-#include "caffe/vision_layers.hpp"
 
 namespace caffe {
 
@@ -48,11 +48,25 @@ void HDF5DataLayer<Dtype>::LoadHDF5FileData(const char* filename) {
   CHECK_GE(status, 0) << "Failed to close HDF5 file: " << filename;
 
   // MinTopBlobs==1 guarantees at least one top blob
-  int num = hdf_blobs_[0]->num();
+  CHECK_GE(hdf_blobs_[0]->num_axes(), 1) << "Input must have at least 1 axis.";
+  const int num = hdf_blobs_[0]->shape(0);
   for (int i = 1; i < top_size; ++i) {
-    CHECK_EQ(hdf_blobs_[i]->num(), num);
+    CHECK_EQ(hdf_blobs_[i]->shape(0), num);
+  }
+  // Default to identity permutation.
+  data_permutation_.clear();
+  data_permutation_.resize(hdf_blobs_[0]->shape(0));
+  for (int i = 0; i < hdf_blobs_[0]->shape(0); i++)
+    data_permutation_[i] = i;
+
+  // Shuffle if needed.
+  if (this->layer_param_.hdf5_data_param().shuffle()) {
+    std::random_shuffle(data_permutation_.begin(), data_permutation_.end());
+    DLOG(INFO) << "Successully loaded " << hdf_blobs_[0]->shape(0)
+               << " rows (shuffled)";
+  } else {
+    DLOG(INFO) << "Successully loaded " << hdf_blobs_[0]->shape(0) << " rows";
   }
-  DLOG(INFO) << "Successully loaded " << hdf_blobs_[0]->num() << " rows";
 }
 
 template <typename Dtype>
@@ -81,9 +95,24 @@ void HDF5DataLayer<Dtype>::LayerSetUp(const vector<Blob<Dtype>*>& bottom,
   CHECK_GE(num_files_, 1) << "Must have at least 1 HDF5 filename listed in "
     << source;
 
+  file_permutation_.clear();
+  file_permutation_.resize(num_files_);
+  // Default to identity permutation.
+  for (int i = 0; i < num_files_; i++) {
+    file_permutation_[i] = i;
+  }
+
+  // Shuffle if needed.
+  if (this->layer_param_.hdf5_data_param().shuffle()) {
+    std::random_shuffle(file_permutation_.begin(), file_permutation_.end());
+  }
+
   // Load the first HDF5 file and initialize the line counter.
-  LoadHDF5FileData(hdf_filenames_[current_file_].c_str());
+  LoadHDF5FileData(hdf_filenames_[file_permutation_[current_file_]].c_str());
   current_row_ = 0;
+  if (this->layer_param_.hdf5_data_param().shuffle()) {
+    std::random_shuffle(file_permutation_.begin(), file_permutation_.end());
+  }
 
   // Reshape blobs.
   const int batch_size = this->layer_param_.hdf5_data_param().batch_size();
@@ -104,22 +133,29 @@ void HDF5DataLayer<Dtype>::Forward_cpu(const vector<Blob<Dtype>*>& bottom,
       const vector<Blob<Dtype>*>& top) {
   const int batch_size = this->layer_param_.hdf5_data_param().batch_size();
   for (int i = 0; i < batch_size; ++i, ++current_row_) {
-    if (current_row_ == hdf_blobs_[0]->num()) {
+    if (current_row_ == hdf_blobs_[0]->shape(0)) {
       if (num_files_ > 1) {
         ++current_file_;
         if (current_file_ == num_files_) {
           current_file_ = 0;
+          if (this->layer_param_.hdf5_data_param().shuffle()) {
+            std::random_shuffle(file_permutation_.begin(),
+                                file_permutation_.end());
+          }
           DLOG(INFO) << "Looping around to first file.";
         }
-        LoadHDF5FileData(hdf_filenames_[current_file_].c_str());
+        LoadHDF5FileData(
+            hdf_filenames_[file_permutation_[current_file_]].c_str());
       }
       current_row_ = 0;
+      if (this->layer_param_.hdf5_data_param().shuffle())
+        std::random_shuffle(data_permutation_.begin(), data_permutation_.end());
     }
     for (int j = 0; j < this->layer_param_.top_size(); ++j) {
-      int data_dim = top[j]->count() / top[j]->num();
+      int data_dim = top[j]->count() / top[j]->shape(0);
       caffe_copy(data_dim,
-          &hdf_blobs_[j]->cpu_data()[current_row_ * data_dim],
-          &top[j]->mutable_cpu_data()[i * data_dim]);
+          &hdf_blobs_[j]->cpu_data()[data_permutation_[current_row_]
+            * data_dim], &top[j]->mutable_cpu_data()[i * data_dim]);
     }
   }
 }
diff --git a/src/caffe/layers/hdf5_data_layer.cu b/src/caffe/layers/hdf5_data_layer.cu
index 02e3821d104..5e3e4ced141 100644
--- a/src/caffe/layers/hdf5_data_layer.cu
+++ b/src/caffe/layers/hdf5_data_layer.cu
@@ -10,9 +10,9 @@ TODO:
 #include "hdf5.h"
 #include "hdf5_hl.h"
 
+#include "caffe/data_layers.hpp"
 #include "caffe/layer.hpp"
 #include "caffe/util/io.hpp"
-#include "caffe/vision_layers.hpp"
 
 namespace caffe {
 
@@ -21,22 +21,29 @@ void HDF5DataLayer<Dtype>::Forward_gpu(const vector<Blob<Dtype>*>& bottom,
       const vector<Blob<Dtype>*>& top) {
   const int batch_size = this->layer_param_.hdf5_data_param().batch_size();
   for (int i = 0; i < batch_size; ++i, ++current_row_) {
-    if (current_row_ == hdf_blobs_[0]->num()) {
+    if (current_row_ == hdf_blobs_[0]->shape(0)) {
       if (num_files_ > 1) {
         current_file_ += 1;
         if (current_file_ == num_files_) {
           current_file_ = 0;
+          if (this->layer_param_.hdf5_data_param().shuffle()) {
+            std::random_shuffle(file_permutation_.begin(),
+                                file_permutation_.end());
+          }
           DLOG(INFO) << "Looping around to first file.";
         }
-        LoadHDF5FileData(hdf_filenames_[current_file_].c_str());
+        LoadHDF5FileData(
+            hdf_filenames_[file_permutation_[current_file_]].c_str());
       }
       current_row_ = 0;
+      if (this->layer_param_.hdf5_data_param().shuffle())
+        std::random_shuffle(data_permutation_.begin(), data_permutation_.end());
     }
     for (int j = 0; j < this->layer_param_.top_size(); ++j) {
-      int data_dim = top[j]->count() / top[j]->num();
+      int data_dim = top[j]->count() / top[j]->shape(0);
       caffe_copy(data_dim,
-          &hdf_blobs_[j]->cpu_data()[current_row_ * data_dim],
-          &top[j]->mutable_gpu_data()[i * data_dim]);
+          &hdf_blobs_[j]->cpu_data()[data_permutation_[current_row_]
+            * data_dim], &top[j]->mutable_gpu_data()[i * data_dim]);
     }
   }
 }
diff --git a/src/caffe/proto/caffe.proto b/src/caffe/proto/caffe.proto
index 888371dc778..5b21cf20028 100644
--- a/src/caffe/proto/caffe.proto
+++ b/src/caffe/proto/caffe.proto
@@ -518,6 +518,13 @@ message HDF5DataParameter {
   optional string source = 1;
   // Specify the batch size.
   optional uint32 batch_size = 2;
+
+  // Specify whether to shuffle the data.
+  // If shuffle == true, the ordering of the HDF5 files is shuffled,
+  // and the ordering of data within any given HDF5 file is shuffled,
+  // but data between different files are not interleaved; all of a file's
+  // data are output (in a random order) before moving onto another file.
+  optional bool shuffle = 3 [default = false];
 }
 
 // Message that stores parameters used by HDF5OutputLayer