Understanding the genetic variation among ear rot/mycotoxin resistant maize inbred lines would greatly aid in breeding high yielding and stable ear rot and mycotoxin resistant hybrids. This study was executed with the objective to characterize ear rot resistant maize inbred lines using phenotypic traits. Experiments were conducted at Ukulinga and Makhathini Research Stations in South Africa. Genetic variability study revealed a significant difference among the mycotoxin resistant inbred lines for Aspergillus ear rot, Fusarium ear rot and other selected secondary traits except for husk cover. Plant height, ear height and primary tassel branches recorded higher heritability estimates (81.6, 81.2 and 82.8%, respectively) compared to all the traits. The principal component analysis clustered the ear rot resistant inbred lines into five groups over the quadrants based on their phenotypic characteristics within the family. The information generated from this study will assist in developing local hybrids with high resistance to ear rots and mycotoxin contaminations, which attribute better agronomic performance.