The often exacting process of isolating intact total RNA from tissue becomes even more difficult when processing certain problematic tissues. Fibrous tissues and tissues rich in protein, DNA and nucleases present distinct challenges for total RNA isolation. Some of the demanding tissues requiring more manipulation and fine-tuning during the RNA isolation procedure are heart, brain, thymus and spleen. Here we address problems we have encountered, and offer troubleshooting techniques to help overcome problems associated with isolating total RNA from difficult tissues. The tips provided are based on RNA isolation by a guanidinium thiocyanate/acid phenol:chloroform extraction method (e.g. Ambion's ToTALLY RNA™ Kit). Note that many of these techniques can be used with other RNA isolation protocols as well.