The immune status of season-independent Atlantic salmon smolt may be affected by changes in photoperiod and high rearing temperatures. Variations in different leucocyte subpopulations were measured in photo-manipulated out-of-season (0+) Atlantic salmon smolt by use of flow cytometry and specific monoclonal antibodies. 0+ smolts were produced by exposing parr to continuous light (LD 24:0) until June 10 followed by a “winter” photoperiod (LD 12:12) for 6 weeks, and then continuous light. Three different groups were studied; untreated smolt (UT), smolt injected with a commercial multivalent oil-adjuvanted vaccine (VA), and smolt injected with the saline/oil-adjuvant used in the vaccine (AD). The fish were injected in the “winter” photoperiod. From introduction of “winter” photoperiod until 2 weeks after seawater transfer, fractions of B-cells (identified by G2H3), neutrophiles (identified by E3D9) as well as polymorphonuclear and B-cells (identified by C4B6) were monitored. From introducing continuous photoperiod and until seawater transfer, there were variations for all groups within the leucocyte subpopulations identified by the monoclonal antibodies (MAb) used. Neutrophiles had a minor increase, while the number of B-cells decreased. C4B6, identifying both types of cells recognised by E3D9 and G2H3 remained stable, indicating that the leucocyte fraction identified by C4B6 was not changed, but there was redistribution with respect to the numbers of B-cells and neutrophiles. After seawater transfer, another redistribution of leucocytes took place. A minor reduction for the neutrophiles was observed, while at the same time, both B-cells and the polymorphonuclear cells increased. It was not possible to identify any effect of vaccine and/or adjuvant on the leucocytes studied. The specific serum antibody levels measured by enzyme-linked immunosorbent assay (ELISA) were low during the experimental period. A low immune response was observed measured as antibody-producing cells (APC) by ELISPOT. The low levels of specific antibodies supported the findings of low APC numbers. There were indications that UT had lower numbers of APC compared to AD and VA. The results show that changes with respect to fractions of leucocyte populations take place during parr–smolt transformation, and these changes may affect the cellular and humoral immune response to vaccination. Different photoperiod regimes may have different effects on leucocyte populations and general conclusions should not be made from the single photoperiod studied.