We evaluated the transduction efficacy of adeno-associated viruses (AAVs) carrying the green fluorescent protein (GFP) marker gene under three distinct promoters—CAG, synapsin, and the mouse choline acetyltransferase (Chat) promoter—in cholinergic and parvalbumin-positive (PV+) neurons within the medial septal area of mice and rats. We quantified the proportion of Chat-positive and PV+ neurons expressing GFP in both species. In mice, the CAG and synapsin promoters demonstrated extremely low efficacy for GFP expression in Chat-positive neurons but were highly effective in transducing PV+ neurons. In contrast, these promoters were equally effective in transducing both Chat-positive and PV+ neurons in rats. The Chat promoter yielded moderate GFP expression in cholinergic neurons in mice, with negligible expression in PV+ neurons, though it also led to off-target expression in other cell types. In rats, the Chat promoter produced moderate GFP expression in both cholinergic and PV+ neurons; however, the majority of GFP-expressing cells were unrelated to these specific neuronal subtypes.