Cytogenetic and molecular cytogenetic analyses, which aim to detect chromosome abnormalities, are routinely performed in cytogenetic laboratories all over the world. Traditional cytogenetic studies are performed by analyzing the banding pattern of chromosomes, and are complemented by molecular cytogenetic techniques such as fluorescent in situ hybridization (FISH). To improve FISH application in cytogenetic analysis the issues with long experimental time, high volumes of expensive reagents and requirement for trained technicians need to be addressed. The protocol has recently evolved towards on chip detection of chromosome abnormalities with the development of microsystems for FISH analysis. The challenges addressed by the developed microsystems are mainly the automation of the assay performance, reduction in probe volume, as well as reduction of assay time. We present here our efforts to introduce automation in the cytogenetic laboratories at a microscale. We have developed membrane based micro perfusion systems capable of expansion of lymphocytes in a shorter time and at a smaller scale. The simulated and experimental results show very efficient exchange of the growth medium to the hypotonic solution and fixative. These are commonly used solutions required for proper preparation of a metaphase chromosomes analysis. Further we developed a microfluidic chip for preparation of metaphase chromosome spreads and their analysis by metaphase FISH on chip. All developed devices are capable of performing the entire metaphase FISH protocol in a shorter time and at the same quality as standard methods.