This study was conducted to investigate how irrigation systems alter root elongation, root morphology, shoot growth characteristics and yield of `TAM-M' jalapeno pepper seedlings. Transplants were grown in containerized trays (18 cm3/cell) for 6 weeks in a greenhouse in Spring 1991. Irrigation systems were: a) floatation (FI), b) 4-week floatation plus 2-week overhead (FI+OI); c) alternate floatation and overhead (FI/OI), and d) overhead (OI). The growing media was maintained between 50 and 20% of its water holding capacity. Between 20 and 41 days after seeding (DAS), FI and FI/OI transplants maintained a constant lateral root length increase. In both FI+OI and OI transplants, lateral root elongation response tended to a `plateau' at ≈ 31 DAS. However, between 31 and 41 DAS, OI transplants had a root growth compensation, increasing the number and length (33%) of basal roots. In FI+OI transplants, basal root growth compensation occurred later in the field. At planting, OI transplants had higher shoot/root ratio (S:R=5) and maintained a higher shoot water potential (ψ= -0.58 MPa) than FI transplants (S:R=3; ψ= -0.69 MPa), respectively. Overhead-irrigated transplants had higher early fruit yields than floatation-irrigated transplants, but total yields were unaffected.