InDrosophila, protein trap strategies provide powerful approaches for the generation of tagged proteins expressed under endogenous control. Here, we describe expression and functional analysis to evaluate newUbxandhthprotein trap lines generated by the Cambridge Protein Trap project. Both protein traps exhibit spatial and temporal expression patterns consistent with the reported endogenous pattern in the embryo. In imaginal discs, Ubx-YFP is expressed throughout the haltere and 3rd leg imaginal discs, while Hth-YFP is expressed in the proximal regions of haltere and wing discs but not in the pouch region. TheUbx^CPTI000601line is semilethal as a homozygote. No T3/A1 to T2 transformations were observed in the embryonic cuticle or the developing midgut. The homozygous survivors, however, exhibit a weak haltere phenotype with a few wing-like marginal bristles on the haltere capitellum. Althoughhth^CPTI000378is completely lethal as a homozygote, thehth^CPTI000378/hth^C1genotype is viable. Using a hth deletion(Df(3R)BSC479)we show thathth^CPTI000378/Df(3R)BSC479adults are phenotypically normal. No transformations were observed inhth^CPTI000378,hth^CPTI000378/hth^C1, orhth^CPTI000378/Df(3R)BSC479embryonic cuticles. We have successfully characterised the Ubx-YFP and Hth-YFP protein trap lines demonstrating that the tagged proteins show appropriate expression patterns and produce at least partially functional proteins.