The major surface glycoprotein (MSG) is an abundant, immunodominant protein on the surface of the opportunistic pathogen Pneumocystis carinii. The current study identified two novel variant MSG (vMSG) gene families in rat P. carinii that are closely related to but distinct from MSG. These gene families encode proteins of ∼90 kDa (v1MSG) and ∼115 kDa (v2MSG). Compared with MSG, v1MSG is characterized by a deletion near the carboxyl terminus. The predicted v1MSG and v2MSG proteins are highly homologous to MSG at the carboxyl, but not the amino, terminus. Like MSG, they are cysteine-rich. Approximately 10% of the apparent molecular weight is due to N-linked glycosylation. Southern blotting studies demonstrated that, like MSG, v1MSG and v2MSG are the products of multicopy gene families. However, unlike MSG, each vMSG gene encodes a signal peptide, suggesting that the regulation of vMSG is different from that of MSG.