Plasmodium falciparum possesses two multigenic families, var and rif, the products of which are expressed on the surface of infected erythrocytes, where via antigenic variation they contribute to malaria pathogenesis and evasion of antibody-mediated host immunity. The products of two smaller gene families, stevor and Pfmc-2TM, also localize to the erythrocyte membrane, although it is not known if they undergo antigenic switching. Herein we use gene-specific quantitative reverse transcription polymerase chain reaction (RT-PCR) to investigate the transcription pattern of the stevor and Pfmc-2TM gene families, in both primary and second generation clonal lines of the P. falciparum isolate, NF54. We show that: (i) the expression of stevor and Pfmc-2TM families is clonally variant, (ii) the expression of stevor and Pfmc-2TM families undergoes switching, and (iii) switching rates vary among different variants and different isogenic clones at rates higher than 2% per generation. In addition, we show that chromosomal telomeric deletions are common in clonal lines and result in a spectrum of deletion genotypes. These findings provide evidence that the stevor and Pfmc-2TM gene families play a role in P. falciparum antigenic variation.