An experiment was conducted to evaluate the genetic diversity of Bt cotton germplasm through morphological and within-boll yield attributes at the experimental area of the University of Agriculture, Faisalabad, Pakistan, during 2015-16 crop season. The experiment was carried out in randomized complete block design (RCBD) with two replications. Genetic diversity assessment among 60 Bt cotton genotypes is studied using principle component analysis (PCA). The coefficient of variance, genetic advance, and heritability have been estimated for each trait. Analysis of variance showed the significant variation among the genotypes for all the traits under investigation. Highest heritability and genetic advance were recorded for bolls per plant and lint mass per boll. In PCA, first five PCs exhibited more than one Eigen value. In PC-I, sympodial branches, monopodial branches, bolls per plant and seed cotton yield per plant were the most important traits contributing 26.15% in the total variation obtained. The variation of 18.87% in PC-II was mainly contributed by node number for the first fruiting branch, node number for first effective boll formation, node height up to first fruiting branch, boll weight and the lint mass per boll. The high genetic variability, heritability and high to moderate genetic advance indicated that germplasm contains genetic potential to be utilized for the future breeding program to develop high yielding cultivars.