Abstract Flow cytometry (FCM) has been used repeatedly to study lectin binding to whole cells. However, there are very few attempts to analyze glycoconjugates in isolated subcellular organelles. We have applied FCM to quantitate the specific binding of fluorescein-conjugated concanavalin A (FITC-Con A) to isolated cis and trans fractions of rat liver Golgi complex, the cell compartment involved in glycoprotein maturation and sorting. Our results show similar intensities of Con A-specific binding in the two fractions. Using this method we show a decreased FITC-Con A binding to both Golgi fractions in ethanol-treated rats, which is consistent to previous work on alcoholic effects on galactosyltransferase. The possible applications of this technique are discussed.