The disease control efficacy of four commonly recommended fungicides: carbendazim (Bavistin, 50 w.p.), carboxin (Vitavax, 75 w.p.) quintozene (Brassicol, 75 w.p.) and thiram (Thiride, 75 w.p.) used as seed treatment, pre‐ and post‐sowing soil drench and seed treatment plus soil drench were tested against wilt and root rot diseases of cotton in multiple sick plots having four soil pathogen:Fusarium oxysporumsp.vasinfectum(Atk.) Snyder and Hansen,Macrophomina phaseolina(Tassi) Goid=Rhizoctonia bataticola(Taub.) Butler,Rhizoctonia solani(Kühn) andFusarium solani(Mart.) Sacc. It was observed that seed treatment or soil application of carbendazim followed by carboxin gave good disease control against pre‐ and post‐ emergence seedling mortality. Pre‐sowing soil drench of test fungicides provided better disease control compared to post‐sowing soil drench. No significant differences in disease control was noted when the test chemicals were used either as seed treatment + pre‐sowing soil drench or seed treatment + post‐sowing soil drench except in carboxin which gave relatively better disease control when used as seed treatment + pre‐sowing soil drench. It is suggested that seed treatment or pre‐sowing soil drench with carbendazim or carboxin could be used to reduce seedling mortality of cotton due to individual or combined infections ofFusarium, MacrophominaandRhizoctoniaspp.