Smoking of non-cigarette tobacco products is increasing worldwide because of their high social acceptability, misperceptions about their purported harmlessness, and globalization of the tobacco industry. In Brazil, tobacco control experts have recently focused their attention on the importance of monitoring the use of such products. We analyzed data from the Global Youth Tobacco Survey (2009) in three cities. Prevalence rates of non-cigarette tobacco smoking in the previous 30 days among students 13 to 15 years of age were high in Campo Grande (18.3%; 95%CI: 14.4%-22.9%) and São Paulo (22.1%; 95%CI: 19.0%-25.6%), while Vitória showed comparatively lower prevalence (4.3%; 95%CI: 3.1%-5.7%). No statistical differences were observed in prevalence rates according to gender. Water pipes were the most frequent form of non-cigarette tobacco smoking. The decline in cigarette smoking in Brazil in recent years may have contributed to other forms of tobacco smoking, especially among students.