We analyze the funding sources for innovation activities in Colombia. Our main objective is to identify the type of capital structure followed by firms performing R&D activities, whether they follow a pecking order (POT) or an altered pecking order capital structure (APOT). We use a multivariate probit methodology and our main result is the fact that innovative companies in Colombia, tend to finance their innovation ventures using a capital structure like the one predicted by the POT. Our results reinforce the fact that innovative companies of underdeveloped countries are, to some extent, different from those of developed countries, and therefore, strategies and policies directed to surpass financial barriers in underdeveloped nations, should be different from the ones designed for developed ones.