Potato virus Y (PVY) and potato leafroll virus (PLRV) are two major viruses which reduce 10-90 percent of yield and quality of potato tubers. In the present study, the efficiency of different methods, including meristem culture, thermotherapy followed by meristem culture and electerotherapy followed by meristem culture in two cultivars (Agria and Marfona) infected by PLRV or PVY were evaluated. Each virus elimination method performed as a factorial experiment basis on a randomized complete block design and for virus elimination methods the combined analysis was used. The percentage of virus elimination was determined by ELISA and RT-PCR, respectively. The percentage of plant regeneration and some agronomic traits, including stem length, stem diameter, shoot fresh weight, number of nodes, internode lenght, number of minitubers, tuber weight and total tuber weight were investigated in virus-free seedlings. The interaction effects were significant for the percentages of plant regeneration and virus elimination method. The highest rate of plant regeneration was obtained in meristem culture method (70%). The highest rate of virus elimination was observed in thermotherapy followed by meristem culture (88%). In this study, three-way interaction of cultivar, virus and method for virus elimination efficiency was significant and the highest virus elimination efficiency (64%) was obtained by the interaction of thermotherapy followed by meristem culture, PVY, for cultivar Marfona. The three-way interaction was also statistically significant for the most agronomic traits. The results of the correlation coefficients, regression and path analysis of yield (number of minitubers per plant) and its related traits showed that the number of nodes per shoot had the highest impact on the number of minitubers in virus-free seedlings.