Many studies on adolescent smoking have been conducted in Malaysia, but very limited information is available on smoking amongst lower secondary school male students (Forms 1 and 2). We present data from a baseline study in Kota Tinggi District, Johor on the psychosocial factors, stages of smoking acquisition and susceptibility to smoking initiation and their relationship to adolescent smoking. The study is the first wave of a 3-year longitudinal study which was conducted from March 2007 to May 2009, aimed to describe the prevalence of smoking among students in the lower secondary classes. A three stage stratified sampling was performed to obtain a sample. The Bogus Pipeline Method was employed to confirm smoking status. Prevalence of smoking was 35.5%. Smoking prevalence among students of schools located in the Federal Land Development Authority (FELDA) settlement areas (42.9%) was two-fold higher than in the rural and town schools combined (20.29%). Using the Fagerstrom scale, 90% of current smokers had lower addiction to nicotine. Smoking was associated with peer smoking [OR, 4.19 (95% CI, 2.57-6.82)], having a brother smoking [2.17 (1.31-3.61)], parental smoking [1.73 (1.17-2.80)] and locality where respondents attend school [1.94(1.11-3.39)]. The study indicates that, the prevalence of smoking was high in all areas especially FELDA settlement areas. Measures such as teaching of skills to resist social pressure to smoke, establishment of peer support groups and involvement of parents in anti-smoking programs are recommended to curb the high prevalence of smoking among lower secondary school students in Kota Tinggi.