diff --git a/Code/Mantid/Framework/Algorithms/src/FFT.cpp b/Code/Mantid/Framework/Algorithms/src/FFT.cpp
index 9e8b57dc78d03be62cf9fbcab0867beb5a2571bf..de33507b44f8936403ad40258a2367cdd5b9c046 100644
--- a/Code/Mantid/Framework/Algorithms/src/FFT.cpp
+++ b/Code/Mantid/Framework/Algorithms/src/FFT.cpp
@@ -181,8 +181,13 @@ void FFT::exec()
   const int ySize = static_cast<int>(inWS->blocksize());
   const int xSize = static_cast<int>(X.size());
 
-  if (iReal >= ySize) throw std::invalid_argument("Property Real is out of range");
-  if (isComplex && iImag >= ySize) throw std::invalid_argument("Property Imaginary is out of range");
+  if(iReal >= ySize) throw std::invalid_argument("Property Real is out of range");
+  if( isComplex )
+  {
+    const int yImagSize = static_cast<int>(inImagWS->blocksize());
+    if( ySize != yImagSize ) throw std::length_error("Real and Imaginary sizes do not match");
+    if( iImag >= ySize ) throw std::invalid_argument("Property Imaginary is out of range");
+  }
 
   //Check that the x values are evenly spaced
   const double dx = (X.back() - X.front()) / (static_cast<int>(X.size()) - 1);