During meiosis, homologous chromosomes are sorted into pairs and are then intimately aligned, or synapsed, along their lengths while a proteinaceous structure, the synaptonemal complex, is assembled between them. However, little is known about how chromosomes first recognise each other. Here we show, by comparing the behaviour of wild-type wheat and wheat mutant for Ph1 (a suppressor of homeologous chromosome pairing), that when chromosomes recognise a partner to pair with, a conformational change to the chromatin is triggered in both partners that is followed by their intimate alignment [corrected]. Thus, a conformational change in the chromosomes at the onset of meiosis can be correlated directly with recognition.