Abstract Several independent genome wide association studies have shown associations of single nucleotide polymorphisms within the C-type lectin domain family 16 member A gene, CLEC16A, with various autoimmune diseases, including systemic lupus erythematosus (SLE). However, the expression and function of this novel C-type lectin domain-containing protein is still largely unknown. This study aims to identify the expressed forms of CLEC16A in peripheral mononuclear cells (PBMCs) and to relate its expression level with SLE disease activity. Two expressed isoforms, isoforms 1 and 2, of CLEC16A have been cloned and sequenced from PBMCs from healthy Chinese, each bearing differences in sequence when compared to the reference sequences derived from Caucasians. In isoform 1, exon 5 was consistently absent in Chinese PBMCs. However, in isoform 2, the stretch of 48-bp in-frame deletion within exon 11 in the reference sequence was found present in Chinese PBMCs. The mRNA expression levels of both isoforms were found significantly lower in SLE patients than in normal individuals. Yet, their expression levels did not correlate with disease activity as measured by SLE disease activity index. The molecular and cellular functions of CLEC16A are currently under investigation, which should shed light on the importance of this protein in SLE pathogenesis.