Crop protection is a part of the agricultural production system. In Europe during the past century, this system has been subject to innovation, stemming from the second agricultural revolution of the Modern Time. Today we are on the crossroad of three alternative agricultural systems. Conventional agriculture is the product of the second agricultural revolution. So far, biotechnological agriculture seems to continue these trends. Organic agriculture on the other hand is a reaction on the paradigm of the second agricultural revolution, especially regarding the negative environmental externalities engendered by this revolution. Today, conventional agriculture is under pressure. Two alternatives have emerged: organic and biotechnological agriculture. Which one is the most economical solution? To answer this question, we analyze these agricultural innovations in a historical perspective, emphasizing the socio-economic evolution process of the production systems during the last century and some of the recent institutional changes. Then we compare short-term micro-economic profitability of conventional versus biotechnological agriculture and conventional versus organic agriculture. To analyze biotechnological agriculture, we refer to two important innovations which have recently been introduced in the Unites States, i.e. glyphosate-resistant soybeans and Bt corn. For the latter, we develop a theoretical micro-economic production model, enabling to represent the effects of Bt corn on total crop protection costs. Finally, we enlarge the scope and compare the macro-economic effects among the three alternatives. The long-term aspects as well as the non-market effects or externalities are taken into account. We conclude the analysis and give some future perspectives. Door middel van een vergelijkende analyse worden de micro- en macro-economische kosten en baten en externaliteiten voor de Europese Unie van drie alternatieve landbouwproductie-systemen afgewogen: gangbare, biotechnologische en biologische. De biotechnologische innovaties blijken valabele alternatieven te bieden voor de gangbare landbouw zowel op micro- als op maco-economische schall, ondanks het feit dat een deel van de voordelen geabsorbeerd wordt door de biotechnologische industrie. De biologische landbouw kenmerkt zich, ondanks haar lagere fysische productiviteit, door een rentabiliteit die vergelijkbaar is met de conventionele landbouw. Ook op macro-economisch vlak heeft dit landbouwsysteem heel wat voordelen te bieden. De toekomst van deze drie landbouwsystemen zal afhangen van hun onderlinge rentabiliteitsverhoudingen, alsook van politieke en sociale factoren, zoals bijvoorbeeld de consumentenhouding ten opzichte van nieuwe technologieen.