Red-fleshed potato (Solanum tuberosum) breeding clones were screened for steroidal glycoalkaloid (SGA) content. SGAs and anthocyanins (ACN) were characterized by HPLC and Mass Spectroscopy (MS). Total SGA ranged from 2.0 to 36.3 mg/100g tuber. Two cultivars with highest anthocyanin content, showed low levels of SGAs. The effect of alkaline treatments on SGA precipitation, anthocyanin content and profile was studied by adjusting the pH of aqueous extracts from 7.6 to 11. Complete removal of SGAs from colored extracts was achieved at pH > 9.2, however it caused substantial anthocyanin loss. Best results were obtained at pH 8.0 with 30% monomeric anthocyanin degradation and 90% SGA precipitation.