In the present study we studied the frequency of MICA polymorphism at GCT repeat of the exon coding for the transmembrane domain and TNFa polymorphism located 3.5 kb upstream of the TNF gene in the Croatian population. Furthermore, the linkage disequilibrium between TNFa, MICA, and HLA loci was examined and extended HLA haplotypes were characterised. One hundred and sixty-five healthy individuals previously typed for HLA class I and class II alleles were tested for 5 MICA alleles and 13 TNFa alleles using an automated sequencer (ALFexpress). The strongest two loci associations were those of MICA-A4 with B*27 and B*18, MICA-A5 with B*15 and B*35, MICA-5.1 with B*0702, B*08 and B*44, MICA-A6 with B*44 and B*51, while MICA-A9 was associated with B*38 and B*35. Analysis of TNFa/HLA-B associations showed the strongest LD values for following combinations: TNFa-a2 with B*08, *15 and *51, TNFa-a6 with B*27, TNFa-a7 with B*44 and *51, TNFa-a10 with B*18, B*35 and B*38 and TNFa-a11 with B*0702. Several extended haplotypes were found with frequency ≥ 0.3%, B*18, -MICA-A4, -TNFa-a10, -DRB1*11 being the most frequent one (0.64%) followed by B*38, -MICA-A9, -TNFa-a10, -DRB1*13 (0.53%) and B*0702, -MICA-A5.1, -TNFa-a11, -DRB1*15 (0.45%). In conclusion, our results provide basic data for the characterization of extended haplotypes with the possible application in disease association studies and unrelated bone marrow transplantation.