Successful experiments in molecular biology require good knowledge about various methods and protocols. In molecular biology, nucleic acid manipulation is the essence, starting with the quality of extraction and ending with several analysis assays (PCR, RT-PCR, qPCR, PCR arrays, molecular cloning, etc). Though many of these are so called “standardized”, in practice there are many variables that can influence the outcome of the experiment. Due to the importance of optimal primer design in PCR assays, we will focus on primer designing and checking software, but we also present other useful free tools that can help researchers in the molecular biology field