Garlic (Allium sativum L.) is a commonly used Allium crop worldwide. It might be expected that garlic would show some intraspecific variations because of its vegetative reproduction. The main goal of this study was to examine the chromosomal aberrations and the relationship between secondary constrictions and nucleolus organizing regions in six garlic clones. Moreover, the biochemical assessments of total protien, esterase and glutamate gxaloacetate transaminase (GOT) were also carried out. Different types of chromosomal aberrations such as chromosome gap, chromatid break, centromeric attenuation and end-to-end association were scored. Data showed that the highest percentage of chromosome gap (15%) was observed in EGA 2 clone. The other structural aberrations were found in different percentages. According to the presence and number and position of the secondary constrictions (SC) and satellites (SAT), four different categories could be identified. Nucleoli number at both the interphase and the prophase showed consederable differences among the six studied clones. For instance, percentage of nucleoli at interphase varied from 94% to 97% (one nuclelus) in Sids 40 and EGA4, respectively. No cells was detected at the prophase containing four nucleoli. A strong relationship was observed between existence of the structural chromosomal aberrations and numbers and position of some cytological markers such as satellites, secondary constrictions and nucleoli. No differences were founed among all studied cloves of the six garlic clones by using total protien, Esterase and GOT. In the present work, the relationship between the assessed biochemical markers and the scored chromosomal aberrations couldn't be proved.