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<h4>Objective</h4>To evaluate the effectiveness of Tobacco Cessation on Prescription (TCP) compared to standard treatment in socioeconomically disadvantaged areas in Swedish primary healthcare (PHC).<h4>Study design</h4>A pragmatic cluster randomized controlled trial, where randomization was conducted at the PHC center level using a computer-generated random allocation sequence.<h4>Setting</h4>18 PHC centers in socioeconomically disadvantaged areas in Stockholm.<h4>Participants</h4>250 adult daily tobacco users (56% female, 41% foreign born) with Swedish social security numbers and permanent resident permits, fluent in Swedish or Arabic, of which 140 responded to the follow-up at 6 months and 139 to the follow-up at 12 months. No blinding was applied.<h4>Interventions</h4>TCP (tobacco cessation counseling for ≥10 minutes, an individualized prescription for tobacco cessation treatment and follow-up on ≥1 occasion) compared to standard treatment.<h4>Primary and secondary outcome measures</h4>The primary outcome was self-reported 7-day abstinence at 6 months and the secondary outcomes included self-reported 7-day abstinence at 12 months and 3-month continued abstinence at 6 and 12 months follow-up.<h4>Results</h4>PHC centers were randomized to the intervention group (n = 8) and control group (n = 10). At the PHC centers, 250 patients (TCP n = 188, standard treatment n = 62) were recruited. There was a statistically significant effect of TCP compared to standard treatment for the outcomes 7-day abstinence at 6 months (OR adjusted 5.4, 95% CI 1.57 to 18.93) and 3-month continued abstinence at 6 (OR adjusted 6.4, 95% CI 1.30 to 31.27) and 12 months follow-up (OR adjusted 7.8, 95% CI 1.25 to 48.82).<h4>Conclusions</h4>TCP may be effective in achieving abstinence from tobacco use compared to standard treatment in the given setting but due to several limitations, resulting in high attrition rates and a low statistical power in the study, more research is needed to evaluate this.<h4>Trial registration</h4>ISRCTN 11498135.