Water deficit increases boll shedding. Large squares, however, are much less likely to shed, possibly because they contain high concentrations of free and total auxin (indole-3-acetic acid or IAA). Our previous research indicated that much of this IAA disappears by the time the squares open as flowers and the IAA content remains low for about 4 days after anthesis. We hypothesized that if water deficit decreased the IAA content, or increased the ABA content, of squares and flowers then water deficit before flowering could have a carry-over effect and increase the shedding rate of young bolls that subsequently develop from them. In field plots water deficit increased the ABA content of flowers as much as 66%. Water deficit first decreased and later increased the concentrations of free and total IAA in squares that were analyzed about 3 days before anthesis. Flowers contained much less IAA than squares. Despite pronounced effects of water deficit on the IAA content of squares it is unlikely that it had any carry-over effect on the free IAA content of young bolls that subsequently developed from them. Water deficit slightly increased the total IAA content of flowers, but had no effect on their free IAA. Because water deficit increased the ABA content but did not decrease the IAA content of flowers, any carry-over effect of water deficit on young boll shedding might have been from changes in ABA but not from changes in IAA.