Clear (CleA) and cloudy (CloA) apple juices containing different amounts of analyzed procyanidins and pectin were investigated for preventive effects of colon cancer and underlying molecular mechanisms in F344 rats given intraperitoneal injections of 1,2-dimethylhydrazine (DMH; 20 mg/kg body wt) once a week for 4 weeks. Rats received either water (Cont), CleA or CloA ( ad libitum ) for 7 weeks starting 1 week before the first DMH injection. CloA inhibited DMH induced genotoxic damage in mucosa cells of the distal colon compared with Cont as investigated by single-cell microgel electrophoresis assay. The mean tail intensity in mucosa cells of DMH-treated controls (Cont/DMH: 6.1 ± 0.9%) was significantly reduced by CloA (2.4 ± 0.8%; P < 0.01) but not by CleA intervention (4.1 ± 1.2%; P > 0.05). The crypt cell proliferation index induced by DMH (Cont/NaCl: 10.0 ± 0.7%; Cont/DMH: 19.9 ± 1.0%; P < 0.001) was significantly decreased by CleA (15.7 ± 0.7%; P < 0.001) and CloA intervention (11.9 ± 0.4%; P < 0.001). CloA but not CleA significantly reduced the number of large aberrant crypt foci (ACF) consisting of more than four aberrant crypts (AC) (Cont/DMH: 37.4 ± 5.4; CleA/DMH: 32.8 ± 4.4, P > 0.05; CloA/DMH: 18.8 ± 2.5 ACF; P < 0.05) and the overall mean ACF size in the distal colon (Cont/DMH: 2.31 ± 0.09; CleA/DMH: 2.27 ± 0.05; CloA/DMH: 2.04 ± 0.03 AC/ACF; P < 0.05). After treatment with DMH and/or apple juices there were no changes in transcript levels of colonic cyclooxygenase isoforms (COX-1, COX-2) or glutathione-associated enzymes (GST-M2, γ-GCS, GST-P), the splenocyte natural killer cell activity and plasma antioxidant status. However, CloA but not CleA prevented the DMH-induced reduction of splenocyte CD4/CD8 (T-helper cells to cytotoxic lymphocytes) ratio. Since both formulations contained comparable concentrations and types of monomeric polyphenols, complex polyphenols or non-polyphenolic compounds, such as pectin might be responsible for the stronger cancer-preventive effect by CloA.