In sub-Saharan Africa, sweetpotato (Impomoea batatas L.) production is greatly constrained by sweetpotato virus disease (SPVD) complex. This study was conducted to assess the incidence of viruses in healthy-looking sweetpotato in Uganda and to optimise modern technologies for virus diagnosis. A collection of healthy-looking sweetpotato vines from central Uganda were serologically assayed for sweetpotato viruses and the positive samples were confirmed by RT-PCR. A multiplex RT-PCR assay was optimised for simultaneous detection of Sweet potato chlorotic stunt virus (SPCSV), Sweet potato feathery mottle virus (SPFMV) and Sweet potato mild mottle virus (SPMMV). The use of in vitro thermotherapy was also investigated as a means of eliminating sweetpotato viruses. Four viruses namely SPCSV, SPFMV, SPMMV and SPCFV were detected mostly as single infections in the healthy looking plants. SPCSV (70. 6%) recorded highest incidence followed by co-infection of SPFMV and SPCSV (8.3%). Based on shoot survival and effectiveness of virus elimination, the best results were obtained by exposing plantlets to daily temperature regime of 32 oC for 8 hr of darkness and 36 oC for 16 hr of light for four weeks. Meristem-tip culture combined with thermotherapy allowed elimination of SPFMV and SPMMV in 77% of plants that were previously infected with the respective viruses. However, elimination of SPCSV was unsuccessful.