Vehicles based on green energy have few takers because of large associated costs. Yet, governments across the world are trying to push for increased usage of alternative energy sources in the automotive sector.

Given this scenario, do green energy stocks (particularly those related to the automotive sector) have the potential to become profitable investments in future? Let's see.

Why green?
There are several reasons why alternative energy companies can rule the roost in the automotive industry in the years to come. According to a report from the Intergovernmental Panel on Climate Change, 77% of the world's energy could come from renewable energy sources by 2050. In the automotive sector, consumers also appear increasingly willing to make a move toward alternative energy sources as the cost of oil increases.

Fuel cells on the rise
FuelCell Energy
(Nasdaq: FCEL) deserves consideration from Fools looking for long-term profits. As the name suggests, the company manufactures fuel cells, which are fast becoming a legitimate energy source of choice for a growing number of consumers in the automotive sector. In the same league is also Enova Systems (AMEX: ENA), which offers fuel cell solutions for hybrid and electric cars.

Biofuels also figure in the list of measures taken to reduce greenhouse gas emissions from vehicles. With growing demand for fuels other than the ones from fossil sources, biofuel should pick up the pace in the automotive world. Producers of biofuel in the U.S. include BioFuel Energy (Nasdaq: BIOF).

Another company that looks lucrative in the biofuel space is Codexis (Nasdaq: CDXS), which makes biocatalysts that expedite the production of biofuels. This company finds even more business in the pharma sector as well. Pfizer (NYSE: PFE), for example, uses its biocatalyst in the production of the blockbuster drug Lipitor. Codexis, I feel, will reap good profits in the near future because of its foray across sectors.

In an earlier article, I discussed how electric vehicles from companies like Tesla Motors (Nasdaq: TSLA) are going to become the transportation of the future. In order to truly understand what drives these vehicles, take a look at the battery under their hood. A major component of this battery is built by Polypore (NYSE: PPO). Its products are also used in Apple products like the iPad. It goes without saying that as the sales of electric vehicles pick up so will the margins of suppliers like Polypore.

Greener in the long run
The automotive industry is on its way to a massive overhaul of the technology it drives on. While concerns regarding greenhouse emissions hound governments across the globe, consumers are worried about rising gasoline prices. The race to find alternatives to the traditional fossil fuel technology is on hyperdrive.

The bottom line
The stocks I mentioned above have the potential to grow with the expansion and development of the alternative energy market for automobiles. In the technology sector, the crucial first mover advantage sometimes determines the winners. But it is still the long run, where the stability of these companies is really put to the acid test. These companies are the early players in a market that is still in its infancy. There is lot more ground that remains to be covered. It will take time before these stocks stabilize. As the attempt to install green, clean energy in our daily lives continues to take off, these stocks are sure to become winners. But as of now, you could start small here in order to cash in on them in the long run.

This article represents the opinion of the writer, who may disagree with the “official” recommendation position of a Motley Fool premium advisory service. We’re motley! Questioning an investing thesis -- even one of our own -- helps us all think critically about investing and make decisions that help us become smarter, happier, and richer.