Field experiments were conducted during 2007-2009 to study the effect of deficit irrigation practices through drip irrigation system on soil moisture distribution and root growth in cotton-maize cropping sequence. Creation of soil moisture gradient is indispensable to explore the beneficial effects of partial root zone drying (PRD) irrigation and it could be possible only through ADI practice in paired row system of drip layout, that is commonly practiced in India. In the present study, PRD and deficit irrigation (DI) concepts (creation of soil moisture gradient) were implemented through alternate deficit irrigation (ADI) at two levels of irrigation using drip system. Experimental treatments comprised of six irrigation levels (full and deficit) through drip system with surface irrigation for comparison. Maize was sown after cotton under no till condition without disturbing the raised bed and drip layout. Roots confined to the shallow depth and recorded the lowest values for both the crops under conventional drip irrigation at 100% ETc. Among the deficit irrigation treatments, mild deficit irrigation produced longer lateral roots from both the sides of the plant. Contrary to rooting depth, severe water stress affected the lateral root spread and recorded lower values than other drip irrigation treatments. Soil moisture content (SMC) was low nearer to the plant (at 30 cm across the lateral) and far away (at 30 cm along the lateral) from the plant, irrespective of treatments. The reduction in SMC was increased at all locations as applied water level decreased. It is concluded that alternate watering imposed through ADI at 100% ETc produced longer lateral roots with higher values for root dry mass Alternate deficit irrigation (ADI) resulted uneven distribution of soil moisture content. Among the ADI treatments, ADI at 100% had less uneven distribution than ADI at 80% ETc.