Loss of ciliated cells and increases in goblet cells are seen in respiratory diseases such as asthma. These changes result in part from reduced differentiation of basal progenitor cells to ciliated cells during injury and repair. The Th2 cytokine, IL-13, has been shown to inhibit ciliated cell differentiation but the mechanism is not clearly understood. We recently showed that Notch signaling inhibits ciliated cell differentiation in submerged culture by repressing multicilin and FOXJ1 expression, genes required for ciliogenesis. Using a novel method to study ciliated cell differentiation we investigated the relationship between IL-13 and Notch signaling pathways. We found that IL-13 inhibits ciliated cell differentiation by repressing multicilin and FOXJ1 expression but does so independent of Notch signaling. In addition, we show that pharmacological inhibition of JAK/STAT but not MEK signaling rescues multicilin and FOXJ1 expression and ciliated cell differentiation in the presence of IL-13. These findings indicate that regulation of multicilin expression by two distinct signaling pathways affects ciliated cell differentiation. In addition, the requirement for JAK activation in IL-13 induced inhibition of ciliogenesis provides a potential therapeutic target for the treatment of respiratory disease.