This paper uses data from PISA 2006 on science, mathematics and reading to analyse immigrant school gaps – negative difference between immigrants’ and natives’ scores - and the structural features of educational systems in two adjacent countries, Italy and France, with similar migration inflows and with similar schooling institutions, based on tracking. Our results show that tracking and school specific programs matter; in both countries, the school system upholds a separation between students with different backgrounds and ethnicities. Residential segregation or discrimination seem also to be at work, especially in France. Given the existing school model, a teaching support in mathematics and science in France and in reading in Italy would help immigrant students to converge to natives’ standards.