The posterior wing is grossly disrupted in en¹/en² transheterozygotes, rarely having an organised fourth or fifth vein. The sex comb on the male prothoracic leg is duplicated posteriorly, more distal leg segments are fused and terminal claws are sometimes missing. The arista and other anterior elements of the antenna are often duplicated. en² in transheterozygous combination with either en⁵⁸ or en⁵⁹ is allows survival to larvae or pharate adults in a few cases. The pharate adults have severe abnormalities in distal segments of all legs and extreme posterior abnormalities in the wing.

Male en²/en³ transheterozygotes show a severe phenotype in the genitalia, which includes the absence of all internal genital organs, the entire penis apparatus, the claspers, the hypandrium, the hypandrial phragma and the lateral process of the genital arch. Extra genital arch and anal plate bristles are sometimes seen. Female flies carrying en² and another en mutation show variable genital abnormalities, ranging from no abnormalities except extra bristles on the eighth tergite and anal plates, to reduced dorsal and ventral vaginal plates, which sometimes have a giant bristle. Extra pigmentation is sometimes seen on the eighth tergite. en²/en³ or en¹/en² flies which are intersex due to a dsx mutation show similar defects in the male or female genitalia as flies which do not carry the dsx mutation.

en¹/en² transheterozygotes have abnormal antennae, the phenotype increasing at higher temperatures (25 or 29^oC). At 29^oC the posterior compartment of the second segment is almost always abnormal, having extra anterior-like bristles which are often arranged in a mirror-image symmetry with respect to the anterior compartment. The third segment is usually larger than normal and is often bilobed. Approximately half the antennae having a bilobed third segment also have an extra arista. en¹/en² transheterozygotes also have abnormal wings; at 17^oC they are grossly enlarged, there is scalloping of the posterior margin, and the triple rows of anterior-like bristles are poorly formed. At 29^oC the wings are not enlarged and a well-formed triple row develops on the posterior margin.

en²/en⁷ flies have reduced viability and severely reduced fertility. en²/Ts(YLt;2Rt)H144+Ts(YSt;2Lt)B107 embryos show extreme disruptions of the denticle belt pattern, some having four denticle belts fused together.