Information on cotton evapotranspiration (ET) during the seedling growth stage and under field conditions is scarce because ET is a difficult parameter to measure. Our objective was to use weighable lysimeters to measure daily values of cotton seedling ET. We designed and built plastic weighable micro-lysimeters (ML) that were 0.35 m deep with a soil volume of 6300 cm³. The soil core was obtained in-situ by pushing the ML well casing into the soil using a commercial soil sampler. The soil core was weighed with tension and compression type load-cells, where a change in mass of 18 g·d^-1 was equivalent to a water evaporation of 1 mm·d^-1. We compared load-cell measurements of changes in mass to values measured with a portable field scale by linear regression analysis, and the slope was equal to 1, indicating no statistical difference (P = 0.05) between the two measurements. We measured and compared seedling height, root length and leaf area of cotton plants in the ML with cotton plants in the surrounding area and this comparison showed that the ML used was suitable to measure cotton seedling ET for the first 30 days after seed emergence. The root mean squared error for crop height was 0.09 cm, for leaf area index (LAI) was 0.03 m²·m^-2 and 6.5 cm for root length. Also, soil temperature at a 0.1 m depth was statistically (P = 0.05) the same in and outside the ML’s. For two planting dates, we measured daily values of soil water evaporation (E) and cotton seedling ET. The day following an irrigation event, E was ~ 9 mm d^-1 and quickly declined the following days. Results showed that ML’s provide an accurate tool to measure water losses from the soil and cotton plants with a LAI of ≤0.2.