Cocoa swollen shoot virus disease (CSSVD) is a major disease of cacao (Theobroma cacao L.) in Ghana and other West African countries that grow the crop. Attempts to develop resistant varieties since the discovery of the disease in 1936 have yielded little success. Recently, planting materials that are tolerant to the disease have been recommended for planting in areas with high CSSVD prevalence. However, the effect of CSSVD on yield component traits of most cacao clones including the tolerant varieties has not been well studied. To investigate the impact of CSSVD on these traits, reduction in bean weight (BW), number of beans per pod (NoBP) and dry bean yield (DBY) between symptomless and symptomatic trees, and disease incidence (DI) among 210 different cacao clones were evaluated. The clones were transplanted in June 2010 following a randomised complete block design with four replications consisting of three trees per clone per block. Response of the clones to CSSVD incidence had 180 of the genotypes having < 50% symptoms. Clones of Contanama, Iquitos, Marañon, Nanay and unknown derived from Upper Amazon parentage had less DI at the end of the study. The CSSVD effect (symptomless vs. symptomatic) was significant (p < 0.05) for DBY and NoBP, and the symptomless trees surpassed on average their symptomatic trees by 21.17% for DBY. Some of the best-performing clones identified under natural CSSVD infection were; COCA 3348/52 and GU 219/V among the underrepresented clones, B 36, ICS 40, NA 33 x IMC 67, T30/628, T60/887, T63/971, T 81/1879 and T 82/503 among those that combine high DBY with low yield reduction, and NA 124, T17/358, T35/78, T57/305, T63/971 x SCA 6, T65/239, T76/1835 and T82/2294 among those that combine high DBY with no disease incidence. Their inclusion in breeding programs that seek to develop resistant CSSVD varieties or deployment as planting materials in endemic areas to improve yield production in Ghana is recommended on the basis of the present observations.