Some morphological and physiological traits of seedlings in eight quince populations from seeds obtained in 2015 (350 progenies per population) were evaluated in 2017 and 2018. They resulted from open pollination of ‘Viduja’, KVD2 and KVD4 genotypes as well as from the crossings of ‘Viduja’ × KVD4, KVD2 × ‘Viduja’, KVD2 × KVD4, KVD4 × ‘Viduja’ and KVD4 × KVD2. Populations showed significant differences in some measured traits, including height and diameter of seedlings, canopy width, annual growth, leaf iron, and chlorophyll content, as well as catalase and peroxidase activities. Based on the results of descriptive statistics, a high variation coefficient was observed in canopy width, peroxidase activity, chlorophyll, and iron content traits. Results of simple correlation showed that there were significant positive correlations between leaf iron content and catalase activity as well as canopy width with both annual growth and leaf length. Cluster analysis among populations based on total traits divided the populations into four distinct groups. The role of the female parents was visible in reciprocal crosses of ‘Viduja’ × KVD4 and KVD2 × KVD4, but all populations with similar female parents were not grouped in the same clusters.