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Background  The outcome of leishmaniasis is an interplay between  Leishamania  and the host. Identifying contributory host genetic factors is complicated by the variability in phenotype, ethnicity and parasite species. Leishmaniasis is caused exclusively by  L. donovani  in Sri Lanka with localized cutaneous leishmaniasis (LCL) being the predominant form. We report here an association study of human leucocyte antigen ( HLA)  class I and II genes with LCL in Sri Lanka, the first on  HLA  associations in cutaneous leishmaniasis in a South Asian population.    Methods  An existing DNA repository of 200 each of patients and controls was typed for  HLA-DQ  by PCR-SSP. Next generation sequencing-based typing for  HLA-A ,  HLA - B  and  HLA - DRB1  alleles was done in a subset of 280 samples. Association tests were performed on 28,489 genotyped and imputed SNPs spanning a region of 1.4 Mb across the  HLA  genes. To compare our results with similar studies, we carried out a systematic review to document all HLA associations reported to-date for cutaneous and muco-cutaneous leishmaniasis.    Results   DRB1*04 DQB1*02  ( P =  0.03;  Pc  = 0.09),  DRB1*07 DQB1*02  ( P =  0.03;  Pc  = 0.09) haplotypes were absent in patients.  B*07  ( P =  0.007;  Pc =  0.13; OR = 0.36; 95 % CI = 0.17–0.77) allele and  DRB1*15 DQB1*06  ( P =  0.00;  Pc  < 0.01; OR = 0.3; 95 % CI = 0.2–.0.6) haplotype were over represented in controls and  DRB1*15  ( P =  0.002;  Pc  = 0.01) allele was over represented in patients. Two SNPs (rs281864595/rs1050517) in the antigen recognition region of  HLA-B , comprised a haplotype more frequent in controls ( P =  0.04). The alleles identified by the systematic review to predispose or to protect from cutaneous/mucocutaneous leishmaniasis remained highly heterogeneous in different populations studied.    Conclusions  Our preliminary findings suggest a role for some class I and class II  HLA  genes in determining predisposition to LCL in this population which should be corroborated with further studies. The systematic review reiterates this need, as the purported susceptibility or protection gained by certain  HLA  alleles or haplotypes has rarely been independently verified.    Electronic supplementary material  The online version of this article (doi:10.1186/s12879-016-1626-8) contains supplementary material, which is available to authorized users.

Association of HLA class I and II genes with cutaneous leishmaniasis: a case control study from Sri Lanka and a systematic review