Earlier studies suggested that traditional apple varieties have quality traits well accepted by consumers and beneficial effects on human health. The aim was to collect 25 traditional apple varieties grown in Croatia and to determine, for the first time in so many details, their external (weight, height, width, shape, color), internal quality traits (firmness, starch decomposition index, maturity index, soluble solid concentration, total acids, soluble solid/total acids ratio, pH), and seed characteristics. In addition, individual polyphenols were determined in the flesh and peel, by using RP-HPLC. All was compared to the commercial variety ‘Idared’. Quality parameters of these varieties were similar to those of the commercial variety. The flesh and peel contained flavan-3-ols, dihydrochalcones, phenolic acids, and flavonols, while anthocyanins were additionally found in the peel. Total polyphenols in the peel (536–3801 mg kg−1 fresh weight (FW)) and in the flesh (79–1294 mg kg−1 FW) of the majority of varieties were higher than in the commercial variety. Principal component analysis showed possible clustering according to polyphenol amounts. According to the observed diversity of quality traits and bioactive polyphenol contents, the traditional varieties have potential for consumer acceptance and increased cultivation.