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Background: Recent advances in whole-genome sequencing and SNP array technology have led to the generation of a large amount of genotype data. Large volumes of genotype data will require faster and more efficient methods for storing and searching the data. Positional Burrows-Wheeler Transform (PBWT) provides an appropriate data structure for bi-allelic data. With the increasing sample sizes, more multi-allelic sites are expected to be observed. Hence, there is a necessity to handle multi-allelic genotype data. Results: In this paper, we introduce a multi-allelic version of the Positional Burrows-Wheeler Transform (mPBWT) based on the bi-allelic version for compression and searching. The time-complexity for constructing the data structure and searching within a panel containing t-allelic sites increases by a factor of t. Conclusion: Considering the small value for the possible alleles t, the time increase for the multi-allelic PBWT will be negligible and comparable to the bi-allelic version of PBWT. [ABSTRACT FROM AUTHOR]