Seaweeds and seaweed extract (SWE) possess antimicrobial, anti-inflammatory, prebiotic, and growth-promoting properties. Extracts can be prepared in different ways including wet, spray-dried, and freeze-dried forms. The aim of this study was to determine if spray drying of laminarin and fucoidan derived from Laminaria digitata had an effect on the microbiological and cytokine profile of the gastrointestinal tract (GIT) compared to the wet SWE in newly weaned pigs. No differences in cytokine expression were observed between wet and spray dried SWE formulation in either the ileum or colon. Bifidobacteria counts were greater (P < 0.05) in the wet SWE formulation relative to both spray dried SWE and the basal diet in the ileum. In conclusion, neither of the SWE formulations had significant effects on the cytokine profile in the ileum or colon. However, a prebiotic effect observed in the ileum of piglets in response to the wet SWE formulation was lost following spray drying of the SWE.