Organic cotton production in Uganda is rising mainly due to the promotional efforts of private multinational cotton exporting companies. Nonetheless, the sustainability of organic cotton projects and their ultimate impact on poverty reduction will depend on the relative profitability of organic cotton production system. This paper therefore attempts to examine the competitiveness of cotton in conventional and organic production systems in Uganda. A survey of 160 cotton farmers was done in Northern Uganda where organic cotton has been introduced. Using whole farm crop budgets and the linear programming method, it was found that cotton was competitive with other ‘cash’ crops only under organic production system mainly because of the existence of price premium. Gross returns to organic cotton were approximately 7%. In the absence of price premium, organic cotton was an unattractive enterprise since farmers made losses of over 13%. Policy recommendations were thus forwarded to promote organic cotton production in Uganda.